Prevent meshes from clipping into each other
If you are referring to what can be seen in the image below, this is called z-fighting. It is when to surfaces overlap and are in the same 3d space. This is not physically possible in the real world. 





To fix this you would have to get rid of one of the overlapping surfaces. 


Select the object Cube
Select the faces that are overlapping.





Delete them, x -> Faces




Final Result